SSAGES supports multiple molecular dynamics engines. However, supported features between MD engines. This may be the result of engine limitations or work in progress. The table below summarizes the main features that vary between supported engines.
|Engine||Supported versions||Multi-walker||NPT virial|
|LAMMPS||2010 or newer||yes||yes|
|Qbox||1.60 or newer||yes||no|
Special instructions on how to use SSAGES with a particular engine are listed under the appropriate section.
SSAGES supports most recent versions of LAMMPS. To compile SSAGES with a
compatible version of LAMMPS, either
-DLAMMPS_SRC=/path/to/LAMMPS must be specified in the cmake command.
cmake -DLAMMPS=YES .. make
will automatically download a recent version of LAMMPS (tagged
and compile SSAGES. Because many users may take advantage of optional LAMMPS
packages, SSAGES forwards the make commands necessary to do so, such
make yes-molecule make yes-user-drude
If a user is interested in using a different version of LAMMPS or one with personal modifications, then SSAGES can be pointed to that particular source repository.
cmake -DLAMMPS_SRC=/path/to/lammps ..
Once you link SSAGES to a particular LAMMPS source, you will be unable to compile that LAMMPS source outside of SSAGES because of SSAGES dependencies which are introduced. Be sure to backup your repository accordingly.
SSAGES integrates with LAMMPS though the flexible fix API offered by LAMMPS. It is therefore necessary to define a SSAGES fix within the LAMMPS input file as follows.
fix ssages all ssages
This directive ensures that SSAGES is able to locate the appropriate adapter and interface with the LAMMPS library. It is very important to name the fix “ssages” as shown above. Otherwise, SSAGES will not work properly. It is highly recommended that the SSAGES fix command be placed after all integrator fixes. Also, make sure tht the fix is specified before the run command, which will begin the advanced sampling simulation.
Due to the nature of how SSAGES forwards commands to LAMMPS, the use
include within a LAMMPS input script is currently not supported.
SSAGES is compatible with typical LAMMPS workflows that include equilibration or energy minimzation steps before production. So long as the SSAGES fix is not declared, LAMMPS will run without any modification.
The only LAMMPS-specific property required in a SSAGES input file is the
property which points to the LAMMPS input script. Details can be found on the
input files page.
SSAGES supports Gromacs versions 5.1.x and 2016.3. To compile SSAGES with a
compatible version of Gromacs, either
-DGROMACS_SRC=/path/to/Gromacs must be specified in the cmake command.
cmake -DGROMACS=YES .. make
will automatically download Gromacs 5.1.3 and compile SSAGES. If a user is interested in using a different version of Gromacs or one with personal modifications, then SSAGES can be pointed to that particular source repository.
cmake -DGROMACS_SRC=/path/to/gromacs ..
Once you link SSAGES to a particular Gromacs source, you will be unable to compile that Gromacs source outside of SSAGES because of SSAGES dependencies which are introduced. Be sure to backup your repository accordingly.